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(v1.6.0.9024) unit test update
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parent
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65
.github/workflows/check.yaml
vendored
65
.github/workflows/check.yaml
vendored
@ -94,11 +94,15 @@ jobs:
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r-version: ${{ matrix.config.r }}
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r-version: ${{ matrix.config.r }}
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- uses: r-lib/actions/setup-pandoc@master
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- uses: r-lib/actions/setup-pandoc@master
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- name: Query dependencies
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- name: Install remotes package
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# if: matrix.config.r != '3.0' && matrix.config.r != '3.1' && matrix.config.r != '3.2'
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if: matrix.config.r != '3.0'
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run: |
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run: |
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install.packages('remotes')
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install.packages('remotes')
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shell: Rscript {0}
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- name: Query dependencies
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run: |
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saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
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saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
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shell: Rscript {0}
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shell: Rscript {0}
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@ -110,28 +114,16 @@ jobs:
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path: ${{ env.R_LIBS_USER }}
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path: ${{ env.R_LIBS_USER }}
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key: ${{ matrix.config.os }}-r-${{ matrix.config.r }}-3-${{ hashFiles('.github/depends.Rds') }}
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key: ${{ matrix.config.os }}-r-${{ matrix.config.r }}-3-${{ hashFiles('.github/depends.Rds') }}
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restore-keys: ${{ matrix.config.os }}-r-${{ matrix.config.r }}-3-
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restore-keys: ${{ matrix.config.os }}-r-${{ matrix.config.r }}-3-
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# - name: Install Linux dependencies
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# if: runner.os == 'Linux' && matrix.config.r != '3.0' && matrix.config.r != '3.1' && matrix.config.r != '3.2'
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# env:
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# RHUB_PLATFORM: linux-x86_64-ubuntu-gcc
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# run: |
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# Rscript -e "remotes::install_github('r-hub/sysreqs')"
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# sysreqs=$(Rscript -e "cat(sysreqs::sysreq_commands('DESCRIPTION'))")
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# sudo -s eval "$sysreqs"
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- name: Install Linux dependencies
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- name: Install Linux dependencies
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if: runner.os == 'Linux'
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if: runner.os == 'Linux'
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# if: matrix.config.r == '3.0' || matrix.config.r == '3.1' || matrix.config.r == '3.2'
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# env:
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# RHUB_PLATFORM: linux-x86_64-ubuntu-gcc
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# update the below with sysreqs::sysreqs("DESCRIPTION") and check the "DEB" entries (for Ubuntu).
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# update the below with sysreqs::sysreqs("DESCRIPTION") and check the "DEB" entries (for Ubuntu).
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# we don't want to depend on the sysreqs pkg here, as it requires a quite new R version
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# we don't want to depend on the sysreqs pkg here, as it requires a quite new R version
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run: |
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run: |
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sudo apt install -y libssl-dev pandoc pandoc-citeproc libxml2-dev libicu-dev libcurl4-openssl-dev
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sudo apt install -y libssl-dev pandoc pandoc-citeproc libxml2-dev libicu-dev libcurl4-openssl-dev
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- name: Install package dependencies
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- name: Update package dependencies using remotes package
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# if: matrix.config.r != '3.0' && matrix.config.r != '3.1' && matrix.config.r != '3.2'
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if: matrix.config.r != '3.0'
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run: |
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run: |
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remotes::install_deps(dependencies = TRUE)
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remotes::install_deps(dependencies = TRUE)
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shell: Rscript {0}
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shell: Rscript {0}
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@ -143,28 +135,8 @@ jobs:
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as.data.frame(utils::installed.packages())[, "Version", drop = FALSE]
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as.data.frame(utils::installed.packages())[, "Version", drop = FALSE]
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shell: Rscript {0}
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shell: Rscript {0}
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# - name: Run R CMD check
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- name: Run R CMD check on Windows
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# if: matrix.config.r != '3.0' && matrix.config.r != '3.1' && matrix.config.r != '3.2'
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# env:
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# _R_CHECK_CRAN_INCOMING_: false
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# _R_CHECK_LENGTH_1_CONDITION_: verbose
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# _R_CHECK_LENGTH_1_LOGIC2_: verbose
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# run: rcmdcheck::rcmdcheck(args = c("--no-manual", "--as-cran"), error_on = "warning", check_dir = "check")
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# shell: Rscript {0}
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- name: Unpack AMR package on Linux and macOS
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if: runner.os != 'Windows'
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run: |
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ls -lh
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tar -xvf data-raw/AMR_latest.tar.gz
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- name: Unpack AMR package on Windows
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if: runner.os == 'Windows'
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if: runner.os == 'Windows'
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run: |
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tar -xvf data-raw/AMR_latest.tar.gz
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- name: Run R CMD check
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# if: matrix.config.r == '3.0' || matrix.config.r == '3.1' || matrix.config.r == '3.2'
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env:
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env:
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_R_CHECK_CRAN_INCOMING_: false
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_R_CHECK_CRAN_INCOMING_: false
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_R_CHECK_FORCE_SUGGESTS_: false
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_R_CHECK_FORCE_SUGGESTS_: false
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@ -172,7 +144,22 @@ jobs:
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_R_CHECK_LENGTH_1_CONDITION_: verbose
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_R_CHECK_LENGTH_1_CONDITION_: verbose
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_R_CHECK_LENGTH_1_LOGIC2_: verbose
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_R_CHECK_LENGTH_1_LOGIC2_: verbose
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run: |
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run: |
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R CMD check AMR --no-manual --no-build-vignettes
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tar -xf data-raw/AMR_latest.tar.gz
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R CMD CHECK AMR -no-manual -as-cran
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shell: bash
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- name: Run R CMD check on Linux and macOS
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if: runner.os != 'Windows'
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env:
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_R_CHECK_CRAN_INCOMING_: false
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_R_CHECK_FORCE_SUGGESTS_: false
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_R_CHECK_DEPENDS_ONLY_: true
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_R_CHECK_LENGTH_1_CONDITION_: verbose
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_R_CHECK_LENGTH_1_LOGIC2_: verbose
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run: |
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tar -xf data-raw/AMR_latest.tar.gz
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R CMD CHECK AMR --no-manual --as-cran
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shell: bash
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- name: Show testthat output
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- name: Show testthat output
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if: always()
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if: always()
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@ -1,5 +1,5 @@
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Package: AMR
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Package: AMR
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Version: 1.6.0.9023
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Version: 1.6.0.9024
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Date: 2021-05-13
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Date: 2021-05-13
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Title: Antimicrobial Resistance Data Analysis
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Title: Antimicrobial Resistance Data Analysis
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Authors@R: c(
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Authors@R: c(
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2
NEWS.md
2
NEWS.md
@ -1,4 +1,4 @@
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# `AMR` 1.6.0.9023
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# `AMR` 1.6.0.9024
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## <small>Last updated: 13 May 2021</small>
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## <small>Last updated: 13 May 2021</small>
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### New
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### New
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@ -27,6 +27,7 @@
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# able to install it. Yet, we want basic R CMD CHECK's in those R versions
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# able to install it. Yet, we want basic R CMD CHECK's in those R versions
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# as well, so only run unit tests in later R versions:
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# as well, so only run unit tests in later R versions:
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if (require("testthat", warn.conflicts = FALSE)) {
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if (require("testthat", warn.conflicts = FALSE)) {
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library(testthat)
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library(AMR)
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library(AMR)
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test_check("AMR")
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test_check("AMR")
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}
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}
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